Various arrays of polynucleotides (such as RNA and DNA) are known and used in genetic testing, screening and diagnostics. Arrays are defined by the regions of different biopolymers or nucleotides arranged in a predetermined configuration on a substrate. Most importantly, the arrays when exposed to a population of analytes will exhibit a pattern indicative of the presence of the various components separated spatially. Array binding patterns of polynucleotides and/or peptides can be detected by using a variety of suitable target labels. Once bound to the array, these target labels can then be quantified and observed and the overall pattern on the array determined.
A number of methods have been designed for manufacturing micro arrays. DNA micro arrays are particularly useful for analyzing large sets of genes through “gene expression profiling”. Using various techniques, arrays can be used to effectively analyze genomes and portions of genomes. Probe arrays have been produced by a variety of means. However, two major methods exist for fabricating arrays used in expression profiling. The first technique uses chemical methods to synthesize polynucleotide probes in situ on array surfaces. This technique uses addressable adaptations of phosphoramidite chemistry. In the second method, polynucleotide probes synthesized enzymatically or chemically can be deposited and attached to a surface through covalent or non-covalent means. The enzymatic method is particularly effective in fabricating arrays with larger probes of 100-1000 nucleotides.
A number of steps are used in the fabrication of the micro arrays designed in the in situ process. The first step in the in situ process is to deposit a polymeric layer on top of a glass substrate or similar type material. Once the polymeric layer has been deposited phosphoramidite chemistry is used to build the oligonucleotides on the micro arrays in a step-wise fashion. This is accomplished by adding one monomer at a time until the final polynucleotide is constructed. The steps of construction using these methodologies are well known in the art and generally include a coupling step followed by a series of capping, oxidation and deblocking steps. The final constructed oligonucleotide can then be employed for binding targets of known or unknown sequences.
Other methods are known in the art that can also be used for fabricating micro arrays. For instance, oligonucleotides or oligonucleotide fragments have been deposited directly on polymer surfaces. After the deposition process the deposited oligonucleotides are then subjected to a drying step and final curing step. The curing step includes the application of heat, UV light or other similar physical or chemical methods to cross-link the polynucleotides to the surface. Processes have also been designed in which cDNA is used in place of polynucleotides and their fragments.
The above methods have been employed for constructing micro arrays in various sizes and designs. However, in the fabrication process a number of problems have arisen. Problems are largely due to incorrect fabrication of oligonucleotides, ineffective chemistries, missing or extra nucleotide bases added and degradation of the oligonucleotides on the surface of the micro array(s). As a result, being able to scale up the fabrication process becomes quite difficult. In addition, a number of the micro arrays need to be discarded due to these existing defects. It, therefore, would be desirable to be able to quickly, efficiently and cost effectively fabricate micro arrays that have a lower number of defects or defective designs. These and other problems with the prior art processes and designs are obviated by the present invention. The references cited in this application infra and supra, are hereby incorporated in this application by reference. However, cited references or art are not admitted to be prior art to this application.